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Sun, J.

Publications and source records attributed to Sun, J..

At least 55 records · Page 3Linked to original sources

Sex-linked Lung Estrobolome May Contribute to Pulmonary Hypertension Penetrance of Bmpr2 R899X Mutation via an ET-1high Endoregulatory Macrophage Phenotype

Mutations in the bone morphogenetic protein receptor 2 (BMPR2) are a major genetic driver of pulmonary arterial hypertension (PAH), yet their penetrance is strikingly sex-biased: females are disproportionately affected, while males experience poorer outcomes. While hormonal and chromosomal factors have been implicated, the biological basis for this disparity remains not fully understood. Here, we investigated the role of the lung microbiome in sex-linked PAH pathogenesis. We hypothesized that increased BMPR2 mutation penetrance in females is partly driven by the accumulation of potent vasoactive molecules, such as endothelin-1 (ET-1), in response to lung microbiome dysbiosis. Using humanized Bmpr2+/R899X mice, we integrate lung metagenomics with basic functional immune profiling to show that females develop a distinct microbiome profile, characterized by increased microbial-derived lipopolysaccharide (LPS), potentially fueling the pathogenic effects of the estrogen metabolite 16-hydroxyestrone (16-OHE). These signals converge on macrophages, where co-exposure led to a hyperactivated state characterized by enhanced phagocytosis and ET-1 secretion. Tissue-level analyses confirmed immune cell infiltration and spatial association with elevated ET-1, providing evidence that these factors may contribute to the onset of sex-linked PAH. Taken together, these findings identify a previously unrecognized microbiome-estrogen-immune axis that amplifies BMPR2 dysfunction and provides a mechanistic basis for female-biased disease penetrance.

immunology↗

Mapping the vRNA Interaction with HIV-1 Integrase

A series of critical interactions within the viral core between the viral RNA (vRNA) and HIV-1 Integrase (IN) has previously been reported. In these studies, contact points between vRNA and IN were identified using RNA-seq and MS-based protein foot-printing approaches. Several IN amino acids located in its C-terminal domain (CTD) were found to be essential for vRNA binding and their alanine substitution severely impacted the correct morphogenesis of the matured viral core. Here, we have extended these studies by performing a comprehensive mapping of the IN-vRNA interaction by deploying RNA crosslinking and NMR methodologies. Together, these approaches were able to identify additional contacts points between the vRNA and IN. Our results reveal several new basic amino acids located in the IN CTD critical for the vRNA-IN interaction, viral replication and correct morphology of the matured viral core.

biochemistry↗

Live Imaging of Epithelial Phagocyte Differentiation in the Drosophila Ovary RevealsTransient and Novel Behaviors

The transformation of epithelial cells into Non-Professional Phagocytes (NPPs) is a conserved and versatile adaptation that occurs in response to immune challenges, tissue remodeling, and apoptotic debris clearance. In the Drosophila melanogaster ovary, follicle cells (FCs) acquire phagocytic capabilities under stress, providing a powerful model to study this process. Using time-lapse live imaging, we captured dynamic behaviors associated with FC-to-NPP differentiation that are too transient to detect by static imaging. Our approach confirmed established features, including germline cell death, cytoplasmic expansion, and debris engulfment, and revealed previously unrecognized capabilities. These include a gradual increase in JNK pathway activation, after which NPPs exhibit collective migration toward dying germline cells, epithelial delamination, long-range target capture through pseudopodial extensions, and the engulfment of neighboring FCs. These findings demonstrate that epithelial-derived NPPs can perform complex phagocytic tasks typically attributed to professional phagocytes such as macrophages. Our work establishes the Drosophila ovary as a robust in vivo system to uncover conserved and novel aspects of epithelial plasticity and phagocytic function, particularly those involving transient behaviors missed by fixed-sample analyses.

cell biology↗

Quercetin Promotes Adipose Thermogenesis and Metabolic Health

The activation of thermogenesis in brown adipose tissue (BAT) represents a pivotal target for ameliorating disorders of glucose and lipid metabolism. This study sought to elucidate the regulatory effects of quercetin on thermogenesis and glucose-lipid metabolism within brown adipocytes, alongside its underlying molecular mechanisms. The findings demonstrated that quercetin markedly upregulated the expression of uncoupling protein 1 (UCP1), a critical thermogenic protein in brown adipocytes, thereby enhancing cellular thermogenic capacity and effectively mitigating glucose and lipid metabolism disorders. Subsequent mechanistic investigations confirmed that quercetin activated the COX2-PGE2-EP4-UCP1 signaling axis by augmenting the stability of cyclooxygenase 2 (COX2) protein, thus mediating its thermogenic-promoting and metabolism-improving effects. This study identifies quercetin as a potential therapeutic agent for the improvement of glucose and lipid metabolism disorders, uncovers a novel molecular mechanism through which quercetin regulates brown adipocyte thermogenesis, and provides a theoretical and experimental foundation for the application of quercetin in the prevention and treatment of obesity and related metabolic diseases.

molecular biology↗

Phage-based microbiome manipulation reveals ecological interactions within gut communities

Mechanistic understanding of gut ecology is limited by the availability of tools for precise manipulation of microbiome composition. Here, we isolate lytic phages to enable targeted removal of gut commensal Escherichia fergusonii (Ef) from complex, undefined stool-derived in vitro communities. A single phage drove resistance without fitness cost in monoculture, but resistant Ef exhibited reduced fitness in communities, enabling expansion of closely related Proteobacteria. Resistance arose via reversible promoter inversion linked to outer-membrane function. A phage cocktail overcame resistance to achieve Ef knockout across communities with minimal collateral effects. Using knockout communities, we show that Ef is necessary and sufficient for preventing Salmonella invasion. Replacement with an Ef transposon-mutant library revealed that community-specific fitness defects are enriched in genes involved in outer-membrane assembly. Disruption of these genes sensitized Ef to antagonistic community members, highlighting interspecies warfare as a key driver of microbiome ecology. These results establish phage-mediated perturbation as a framework for linking species to community-level function and for enabling precision microbiome engineering.

microbiology↗

A standardized, surgically relevant map of organ-spesific branch emergence in the human vagus nerve

IntroductionVagus nerve stimulation modulates airway, cardiac, pulmonary, and gastrointestinal functions through respective organ-specific branches. Knowledge of where along the nerve vagal branches emerge may support alternative surgical placement of stimulation devices to activate targeted functions while avoiding off-target effects. However, no quantified map of the emergence of vagal branches and their relationship to surgically relevant anatomical landmarks exists in humans. MethodsFifty-eight vagus nerves (29 left, 29 right) from 29 embalmed donor bodies (15 females) were dissected from the jugular foramen through the thoracic cavity. Branches were traced to end organs and allocated to one of seven groups (sympathetic, muscular, vascular, cardiac, pulmonary, esophageal, or multiple targets) and several sub-groups. Distances between branch emergence and jugular foramen (JF) were normalized to three anatomical landmarks: carotid bifurcation, laryngeal prominence, and superior border of clavicle. ResultsEmergence of branches follows a proximal-to-distal order (median [IQR] distance from JF): sympathetic (3.9 cm [3.0-6.6]), muscular (6.2 [3.4-17.0]), vascular (9.6 [5.5-15.1]), cardiac (20.1 [16.9-22.5]), pulmonary (25.0 [22.8-27.6]), and esophageal (26.5 [24.3-29.1]). Branches emerge into two embryological domains separated at the clavicle: pharyngeal arch branches cluster proximally (7.3 cm [3.9-14.0]) and primitive mediastinum branches cluster distally (24.2 cm [20.9-27.1]), with sympathetic, muscular, and vascular sub-groups occupying distinct zones within the proximal domain. The longest branch-free intervals are all left-sided, occurring around the laryngeal prominence (3.0 cm [1.8-5.7]), the superior border of the clavicle (2.7 cm [1.3- 5.2]), and the carotid bifurcation (2.2 cm [0.9-5.7]). Several "target" branches are maximally separated from "off-target" branches at specific distances: sympathetic vs. cervical/ muscular/ vascular at 6/8 cm (L/R), cardiac vs. carotid sinus at 14/10 cm, and recurrent laryngeal vs. other muscular at 18/13 cm. Minimal differences are found between male and female donors. ConclusionThis study describes a quantified, landmark-registered map of cervical and thoracic vagal branch emergence and provides an anatomical reference that may help guide more selective device design and placement.

neuroscience↗

Neuronal regulation of infection recovery prevents pathogenic stress and tissue damage

Neural regulation of immunity is increasingly recognized, yet how the nervous system promotes infection resolution after pathogen clearance remains poorly understood. Using Caenorhabditis elegans, we identify the AIA interneurons as key regulators of both infection and recovery. Acute silencing or genetic ablation of AIA neurons during Salmonella enterica infection reduces host survival, causes excessive activation of conserved immune and stress pathways, including PMK-1/p38 MAPK, insulin/IGF-1 signaling, and the XBP-1-mediated unfolded protein response (UPR), and exacerbates intestinal tissue damage. Strikingly, selective silencing of AIA neurons after pathogen clearance markedly impairs recovery, demonstrating that neural activity is required not only for host defense but also for infection resolution. This defect is rescued by xbp-1, but not pmk-1 or daf-16, knockdown, identifying unresolved ER stress as the principal driver of post-infection mortality. Consistently, AIA silencing during recovery sustains UPR activation and worsens epithelial barrier damage. Together, our findings establish AIA interneurons as central regulators of immune homeostasis that promote infection resolution by limiting excessive ER stress and preserving tissue integrity.

immunology↗

Elucidating the molecular interplay between LRRK2 and Rab GTPases

Gain-of-function mutations in LRRK2 are a major cause of inherited Parkinsons disease. LRRK2 encodes a multidomain kinase, whose bidirectional interplay with Rab GTPases regulates critical cellular processes like lysosomal homeostasis. Certain Rabs, including Rab12 and Rab29, recruit LRRK2 to organelle membranes and stimulate its kinase activity; activated LRRK2 phosphorylates a subset of Rabs in their Switch-II motifs. Molecular basis governing selective Rab recognition by LRRK2 remains unclear. Here we structurally characterize LRRK2 interactions with representative Rab GTPases and identify three novel Rab-binding sites: site 4 for Rab8A/10, site 5 for Rab43, and site 6 for Rab5A, defining a total of six distinct binding sites that account for known LRRK2-interacting Rabs. Additionally, we elucidated the binding site of GABARAP, an ATG8 member that recruits LRRK2 to stressed lysosomes. Our findings provide a framework for therapeutic targeting of LRRK2 recruitment for Parkinsons.

biochemistry↗

Mutation of a single cysteine in CaMKIIδ protects the heart from ischemia-reperfusion Injury

CaMKII{delta} is the dominant isozyme of Ca2+/calmodulin-dependent protein kinase II in the heart. Under certain pathological conditions, it can be oxidized, causing a constitutive activation that can lead to cardiac failure. We recently showed that, in purified CaMKII{delta} exposed to oxidative conditions, a disulfide link formed between Cys273 and Cys290 causes this autonomous activation. Cys273 has a low pKa that facilitates the oxidation of its thiol to a sulfenic acid at physiological pH. Does this matter in vivo? To answer that question, we created a transgenic mouse with Cys273 mutated to serine (CaMKII{delta}C273S) to prevent disulfide formation. We conducted a detailed assessment of cardiac function at rest and in a dobutamine stress test. We found that the CaMKII{delta} Cys273Ser mutation does not have deleterious effects on cardiac physiology. Then, we assessed whether the mutation would protect the heart from ischemia-reperfusion in the Langendorff model. The CaMKII{delta}C273S mouse had improved cardiac function and decreased infarct size compared to the wild-type mouse. We conclude that blocking disulfide formation at Cys273 protects the heart against ischemia-reperfusion injury. Drugs that specifically target Cys 273 may be therapeutic in human cardiac disease.

biochemistry↗

Connections across regional glymphatic clearance, neural activity and amyloid-β deposition in cortex

Neural activity inevitably produces waste, which promotes neurodegeneration with topographic features. The glymphatic system is important for waste clearance. However, the spatial characteristics of glymphatic clearance across cortex and whether it interplays with neural activity in contribution to amyloidosis in human remain unexplored. Here, by intrathecal administration of gadolinium-based contrast agents, glymphatic influx and clearance patterns across cortex in 96 participants are depicted via Glymphatic MRI. Analyses integrating post-mortem transcriptomic profiles from Allen Human Brain Atlas indicate that, genes related with excitatory and inhibitory neurons, and pathways engaging in synaptic function were enriched in regions with faster glymphatic clearance. FALFF was calculated from resting-state fMRI to represent neural activity. At the regional level, based on a subgroup with rs-fMRI (N = 15), regional glymphatic clearance was positively coupled with spontaneous neural activity. Mismatch index, reflecting decoupling between spontaneous neural activity and glymphatic clearance function, turned out to be positively associated with regional severity of amyloidosis using open-source 11C-PiB dataset. Together, this study for the first time demonstrates the intricate interplays between neural activity and glymphatic dynamics from transcriptional to physiological level. The mismatch between these two processes may serve as an undescribed comprehensive mechanism promoting regional vulnerability to proteopathy and subsequent neurodegeneration in cortex.

neuroscience↗

Origin and evolution of grapevine genomes

Grapevines (Vitis) belonging to grape family (Vitaceae) are symbolic fruit crops pivotal to human civilization. The evolutionary history of grapevines divergent from other Vitaceae plants remains mysterious, requiring a family-wide whole-genome phylogenomic analysis. Here, we conduct chromosome-level phylogenomics to investigate the origin and evolution of grapevines using 29 genome assemblies of five genera Vitis, Parthenocissus, Ampelopsis, Tetrastigma, and Cissus, 27 of which are newly released in this study. Phylogenomic and macrosynteny analysis unanimously support Ampelopsis as a sister lineage to Parthenocissus, placing both closer to Vitis, with introgression and incomplete lineage sorting contributing to these relationships. Ancestral genome reconstruction delineates the major chromosome rearrangement events in Vitaceae karyotype evolution, highlighting the conserved karyotype in Vitis and the extensive karyotypic reorganization in Tetrastigma and Cissus. Pan-3D genome analysis highlights the contributions of structural variants (SVs) to the variation of A/B compartments and topologically associated domains (TADs), revealing a strong purifying selection of SVs at TAD boundaries. We further demonstrate that Helitron transposons drive the expansion and expression regulation of NLR immune-receptor genes in Vitis. Importantly, we discovered an NLR gene VbRpv35 from wild grapevine V. bellula resistant to downy mildew (DM), whose heterologous expression in V. vinifera confers enhanced DM resistance. Taken together, we provide phylogenomic insight into the origin and evolution of grapevines and valuable resources for grapevine improvement and understanding angiosperm evolution.

genomics↗

TAR syndrome causal gene RBM8A is critical for embryonic bone development and proper Hedgehog signaling

RNA-Binding Motif Protein 8A (RBM8A) is a core component of the exon junction complex (EJC), which plays a fundamental role in post-transcriptional RNA regulation. Mutations in the RBM8A gene cause thrombocytopenia-absent radius (TAR) syndrome, characterized by reduced platelet number and radial defects. However, how its function contributes to bone development remains poorly understood. We found that RBM8A is highly expressed in human bone marrow-derived mesenchymal stem cells (MSCs) and mouse embryonic limb buds. To further investigate the role of RBM8A in bone development, we generated an Rbm8a conditional knockout mouse (cKO) model in the early limb bud and craniofacial mesenchyme using the Prx1-cre line, which recapitulates key features of TAR syndrome. Rbm8a deficiency in this mouse model resulted in significant defects in limb and craniofacial development, including shorter limb bones across developmental timepoints, delayed ossification, altered cranial morphogenesis, along with impairments in motor function and reduced brain size. To elucidate the molecular basis of these phenotypes, we performed RNA immunoprecipitation sequencing (RIP-seq) in embryonic limb tissue. Our analysis revealed that RBM8A preferentially associates with long, exon-rich transcripts with high isoform complexity. These transcripts are enriched in pathways related to primary cilia, RNA processing, and developmental signaling. Consistent with this, transcriptomic and enrichment analyses identified strong associations with ciliopathy-related and congenital skeletal disease gene sets. At the cellular level, Rbm8a deficiency resulted in altered expression of key chondrogenic and ossification markers in embryonic limb bone tissue, such as reduced SOX9 and increased IHH in the primary ossification center, suggesting impaired progression of endochondral ossification and disrupted Hedgehog pathway activity. Quantitative Reverse Transcription-PCR (qRT-PCR) analysis further validated selective downregulation of Hedgehog pathway targets, including Gli3 and Hhip, while other developmental genes remained unchanged, indicating pathway-specific attenuation. Together, these findings support a model in which Rbm8a regulates structurally complex transcripts that are enriched in ciliary and developmental signaling pathways, and that disruption of this process leads to selective impairment of Hedgehog signaling and skeletal development. These results provide a novel mechanistic link between RNA processing and developmental signaling and offer new insight into how defects in RNA regulation contribute to congenital skeletal abnormalities.

developmental biology↗

OneGenomeRice (OGR): A Genomic Foundation Model for Rice

The transition of genomics to a predictive intelligence discipline is driven by the advent of genomic foundation models. While substantial progress has been observed in all-life and human-centric models, plant species, particularly for the staple crops, remains hindered by a lack of models. Here we introduce OneGenome-Rice (OGR), a rice (Oryza sativa) genomic foundation model pre-trained on a genomic dataset comprising 422 high-quality genomes of cultivated and wild rice. OGR is engineered upon a Mixture of Experts (MoE) transformer architecture with 1.25-billion parameters and supports an ultra-long context window of up to 1 million base (Mb) pairs at single-nucleotide resolution. A comprehensive benchmark demonstrated that OGR significantly outperforms existing state-of-the-art multi-plant or all-life genome models in 11 categories (e.g. motif identification, sweep detection, etc). We further demonstrated the utility of OGR in several downstream applications, such as indica-japonica subspecies introgression analysis, identification of agronomy trait-associated functional loci and prediction of gene expression from DNA sequences. These results establish OGR as a promising foundational computational infrastructure for rice functional genomics and precision breeding. The OGR and its fine-tuned models, including pretrained weights, training code and the rice genomic benchmark suit, have been fully opened.

genomics↗

Leptin Acts as a Peripheral Tropic Signal to Tune Steroidogenesis

The integration of metabolic status with reproductive and developmental timing is a cornerstone of animal physiology, yet how steroidogenesis rapidly adapts to abrupt environmental changes remains poorly understood. Here, we identify a peptide hormone circuit in which leptin or its analogs act as peripheral tropic signals, directly coupling systemic metabolic state to steroid hormone production through dynamic remodeling of intracellular lipid pools. Mechanistically, spatiotemporal fluctuations in leptin activate JAK/STAT signaling within steroidogenic tissues to reprogram the balance among lipid droplets, cholesteryl esters, and free cholesterol, thereby tuning the amplitude and timing of steroid hormone pulses via hormone-sensitive lipase (Hsl), a rate-limiting determinant of steroidogenic flux. Cross-species analyses in Drosophila melanogaster, Blattella germanica, and Mus musculus suggest a partially conserved leptin-JAK/STAT-lipase axis that functions as a metabolic "sterol rheostat", enabling rapid modulation of steroidogenesis in response to systemic metabolic and stress cues. These findings reveal a metabolic-endocrine mechanism by which leptin can act directly on steroidogenic organs to regulate hormonal output.

developmental biology↗

Ultra-sensitive FLORA-seq links cell-type-specific tRNAome dynamics to differentiation trajectories guiding therapeutic suppressor tRNA candidate selection

Mammalian genomes encode hundreds of tRNA genes, but the role of individual tRNAs in development and cell identity remains unclear. Here, we introduce FLORA-seq, a method for simultaneous, low-input profiling of tRNAs, tRNA-derived RNAs (tdRs) and their modifications from as few as 5-20 cells. Applying FLORA-seq to mouse hematopoiesis revealed 50 high-variance isodecoders whose expression profiles recapitulate known hematopoietic cell types and correlate with differentiation trajectories. At the isoacceptor level, tRNA pools are largely stable within hematopoietic stem and progenitor cells (HSPCs), showing only subtle, specific variations, but become both distinct from HSPCs and internally stable within each terminally differentiated lineage. We further detected dynamic changes in tdR ratios and modification patterns, underscoring precise tRNA regulation during differentiation. Crucially, analysis of 54 endogenous tRNA isodecoders and their engineered suppressor counterparts showed that efficient premature termination codon readthrough preferentially arises from highly expressed cognate isodecoders. This correlation provides a rational framework for prioritizing suppressor tRNA candidates and implies non-redundant functions for individual isodecoders.

molecular biology↗

In utero transduction resolves gut cell lineages and enables conditional gene perturbation in the developing enteric nervous system

How diverse cell lineages emerge and are genetically regulated during organogenesis are central questions in understanding the developmental origins of disease. However, the mouse gut, including its intrinsic enteric nervous system (ENS) derived from migratory neural crest, has remained difficult to experimentally target. Here, we introduce an in utero lentiviral nano-injection strategy that enables early and efficient access to progenitor cells of all major cell types within the developing gut as well as gut-innervating ganglia. Leveraging this approach in combination with DNA barcoding and single cell transcriptomics, we resolve clonal relationships in all gut lineages, including epithelial, neural, immune, and mesenchymal cell types. Clonal coupling between distinct subsets of fibroblasts and either pericytes, mesothelial cells, or interstitial cells of Cajal, suggested a developmental logic whereby the mesenchymal compartment arises from a set of fate-biased progenitors. Yet, mesenchymal regionalization along the anterior-posterior axis establishes early, whereas the ENS displays broad clonal dispersion across gut regions and acquires subsequent regional identities. We further adapted the platform for temporally controlled cell-type specific gene manipulation and, as a proof-of-principle, show that induced expression of the proneural factor Ascl1 biases ENS progenitor cells toward neuronal differentiation. Together, this work provides insights into refined spatiotemporal lineage relationships within a multigerm-layer organ and establishes a broadly applicable in vivo framework for probing gene function during gastrointestinal and neural crest development. SIGNIFICANCEThe gastrointestinal tract comprises diverse cell types originating from all three germ layers and includes the neural crest-derived enteric nervous system (ENS). Progress in defining these lineages and their gene regulation is challenged by the limited experimental access to the developing gut. Here, we establish in utero lentiviral transduction as an efficient approach to resolve clonal lineages and address gene functions in defined gut cell types. We show that mesenchyme assumes positional allocation early and differentiates through fate-restricted progenitors, linking specialized mesenchymal cell types to different fibroblasts. In contrast, the ENS differentiates stochastically and acquires late regional identities. Our study reveals fundamental principles of multi-lineage organogenesis and provides a framework to dissect the contribution of developmental programs to visceral dysfunction.

developmental biology↗

Protenix-v2: Broadening the Reach of Structure Prediction and Biomolecular Design

Advances in biomolecular modeling have broadened the range of problems addressable by structure prediction and design models. Here, we present results from Protenix-v2, a system spanning high-accuracy structure prediction and biomolecular design. On the structure prediction side, Protenix-v2 achieves antibody-antigen success rates with up to 13-point gains over Protenix-v1, while 5-seed performance surpasses previous 1000-seed results. On the design side, Protenix-v2 demonstrates a 100% target-level success rate in novelty-controlled VHH-Fc campaigns, reaching hit rates up to 48%. Crucially, the model enables hit discovery on difficult GPCR targets with hit rates of 16%-88% (VHH-Fc) and up to 50% (mAb) under 16-30 testing budgets per target. Resulting hits show high developability and diversity. Beyond antibody tasks, we report improved ligand-related plausibility and successful cross-variant SARS-CoV-2 spike RBD mini-binder design. These results establish Protenix-v2 as a robust and powerful model for accelerated drug discovery.

molecular biology↗

A lateral linker histone binding mode scaffolds dinucleosome stacking in chromatin fibers

Linker histones are essential for chromatin compaction, yet how they contribute to higher-order fiber assembly remains poorly understood. Here, we determined cryo-electron microscopy structures of Arabidopsis dodeca-nucleosome fibers containing distinct H2A/H3 variants and linker histone H1.3, revealing a noncanonical binding mode that a laterally positioned H1.3 connects the acidic patch of one nucleosome and the DNA of the neighboring nucleosome, thereby scaffolding dinucleosomes into two-start chromatin fibers. This noncanonical binding mode is structurally conserved when H1.3 is replaced by Gallus gallus H5. Furthermore, incorporation of H2A.W and H3.3 further induces back-to-back fiber dimerization. Cryo-electron tomography and in vivo cross-linking mass spectrometry analyses support the physiological relevance of H1 lateral engagement. Our findings establish that linker histones act as active architectural scaffolds in higher-order chromatin organization.

molecular biology↗